Some very used but not-uv-intelligent tools are Extrude, Decimate, make faces/edges and Rotate (??).

So, if you need to modify your mesh try to use the intelligent tools as much as possible, and try to limit the use of the not-intelligent tools. In the end chances are that you still will need to fix the UV Mapping by hand, but the less you have to fix the better.

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Speaking of bugs and UV mapping, I just learned that 3.1a does not respond correctly when loading 'from window', however, it is fixed in the current cvs, so if you have been pulling your hair out trying to get your faces to load correctly in the UV window, wonder no more.

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